Created using Colab #191
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| name: PopV | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main] | |
| schedule: | |
| - cron: "0 10 * * *" # runs at 10:00 UTC (03:00 PST) every day | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| timeout-minutes: 40 | |
| defaults: | |
| run: | |
| shell: bash -e {0} # -e to fail on error | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - os: ubuntu-latest | |
| python: "3.10" | |
| - os: ubuntu-latest | |
| python: "3.11" | |
| - os: ubuntu-latest | |
| python: "3.12" | |
| name: ${{ matrix.os }} Python ${{ matrix.python }} | |
| env: | |
| OS: ${{ matrix.os }} | |
| PYTHON: ${{ matrix.python }} | |
| steps: | |
| - name: Set up Git LFS | |
| run: git lfs install | |
| - name: Check out repository | |
| uses: actions/checkout@v4 | |
| with: | |
| lfs: true | |
| - name: Set up Python ${{ matrix.python }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| cache: "pip" | |
| cache-dependency-path: "**/pyproject.toml" | |
| - name: Debug LFS files | |
| run: | | |
| ls -lh resources/dataset/test | |
| file resources/dataset/test/*.h5ad | |
| ls -lh resources/ontology | |
| file resources/ontology/* | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip wheel uv | |
| python -m uv pip install --system "popv[dev,test] @ ." | |
| - name: Test | |
| env: | |
| MPLBACKEND: agg | |
| PLATFORM: ${{ matrix.os }} | |
| DISPLAY: :42 | |
| run: | | |
| coverage run -m pytest -v --color=yes | |
| coverage report | |
| - name: Upload coverage | |
| uses: codecov/codecov-action@v4 |